18 September 2008

ATCC 51142 An Amazing Microbe Full of Promise

These tiny green cyanobacteria may not look like much, but Cyanothece sp. ATCC 51142 is incredibly versatile. In sunlight it uses photosynthesis to produce sugars for energy. At night it fixes nitrogen from the air for making proteins, nucleic acids, and other important molecules. Its genomic makeup is complex for such a simple organism, and Washington University researchers in St. Louis are learning a great deal from the unique organism--using a clever combination of proteomics and genomics.
Cyanobacteria are the only known bacteria to have a circadian clock. By day, Cyanothece cells increase gene expression for photosynthesis and sugar production; at night they moonlight, ramping up gene expression that governs energy metabolism, nitrogen fixation and respiration.

Pakrasi and his collaborators found the presence of a rare linear chromosome in the organism's genome, a first in cyanobacteria...Cyanothece 51142 has one large circular chromosome, a linear chromosome and four small plasmids.

"This is the first time anything like this has been found in photosynthetic bacteria. It's extremely rare for bacteria to have a linear chromosome," said Pakrasi. "Nearly 100 percent of them do not. Now, we have the genome of this organism, which gives us a complete picture of everything that can possibly happen in this cell...Now, we can go back to this complete picture and compare its brother and sister organisms to find their talents and deficiencies. That's comparative genomics," said Pakrasi. _Source
A clever combination of the use of proteomics with genomics allowed the researchers to find more genes than through use of gene sequencing alone.
Proteomics analysis examines almost the whole complement of proteins in a cell, but requires a gene sequence with which to pair up protein shards for identification. On the other hand, DNA sequencing can't always identify potential genes or unmask which of those really function, and could benefit from knowing which proteins the cell actually makes.

Instead of waiting on one analysis to do the other, the collaborators simultaneously sequenced the bacteria's DNA and determined proteins that the microbe produced at different times of its life cycle. They then compared the information to determine which of the DNA sequences that looked like genes actually made proteins. In this way, they could better determine where genes lie along the length of its genome, as well as find ones that might otherwise be missed.

"This was an excellent example of using proteomics to guide initial genomic annotation," said protein chemist Jon Jacobs of PNNL. "We're helping to set a precedent if we can do the proteomics work while they're doing the genomics work."

...In addition to the 2,700-plus real genes, the DNA sequence contained more than 2,500 would-be genes. These had architectural features common to genes but didn't look like recognized genes from other organisms. The team found about 500 of these that produced proteins, so the researchers re-classified these genes as functioning. Lastly, the scientists also found 38 proteins out of another 12,000 sequences that were gene longshots. _SD
In the dark, cyanobacteria can also act as fermenting organisms, producing acetate, ethanol, H2, lactate, etc.

This already impressive work will only grow more sophisticated and productive with time. Using this tiny bacteria as a model organism and comparing it with related strains will bring about an exquisitely fine knowledge of its dynamic function under all conditions of energy, nutrient, and other environmental conditions. Such knowledge will be pivotal in the quest to create better energy and food sources.

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